scholarly journals Were the synapsids primitively endotherms? A palaeohistological approach using phylogenetic eigenvector maps

2020 ◽  
Vol 375 (1793) ◽  
pp. 20190138 ◽  
Author(s):  
Mathieu G. Faure-Brac ◽  
Jorge Cubo
Keyword(s):  
Maximum Likelihood ◽  
Metabolic Rates ◽  
Theme Issue ◽  
Ancestral States ◽  
Extinct Taxon

The acquisition of mammalian endothermy is poorly constrained both phylogenetically and temporally. Here, we inferred the resting metabolic rates (RMRs) and the thermometabolic regimes (endothermy or ectothermy) of a sample of eight extinct synapsids using palaeohistology, phylogenetic eigenvector maps (PEMs), and a sample of 17 extant tetrapods of known RMR (quantified using respirometry). We inferred high RMR values and an endothermic metabolism for the anomodonts ( Lystrosaurus sp., Oudenodon bainii ) and low RMR values and an ectothermic metabolism for Clepsydrops collettii, Dimetrodon sp., Edaphosaurus boanerges, Mycterosaurus sp., Ophiacodon uniformis and Sphenacodon sp. A maximum-likelihood ancestral states reconstruction of RMRs performed using the values inferred for extinct synapsids, and the values measured using respirometry in extant tetrapods, shows that the nodes Anomodontia and Mammalia were primitively endotherms. Finally, we performed a parsimony optimization of the presence of endothermy using the results obtained in the present study and those obtained in previous studies that used PEMs. For this, we assigned to each extinct taxon a thermometabolic regime (ectothermy or endothermy) depending on whether the inferred values were significantly higher, lower or not significantly different from the RMR value separating ectotherms from endotherms (1.5 ml O 2 h −1 g −0.67 ). According to this optimization, endothermy arose independently in Archosauromorpha, Sauropterygia and Therapsida. This article is part of the theme issue ‘Vertebrate palaeophysiology’.

scholarly journals Directional Selection and the Site-Frequency Spectrum

Genetics ◽  
2001 ◽  
Vol 159 (4) ◽  
pp. 1779-1788 ◽  
Author(s):  
Carlos D Bustamante ◽  
John Wakeley ◽  
Stanley Sawyer ◽  
Daniel L Hartl
Keyword(s):  
Maximum Likelihood ◽  
High Power ◽  
Negative Selection ◽  
Likelihood Estimation ◽  
Directional Selection ◽  
Likelihood Ratio Tests ◽  
Maximum Likelihood Estimates ◽  
Likelihood Methods ◽  
Ancestral States ◽  
Asymptotic Variances

Abstract In this article we explore statistical properties of the maximum-likelihood estimates (MLEs) of the selection and mutation parameters in a Poisson random field population genetics model of directional selection at DNA sites. We derive the asymptotic variances and covariance of the MLEs and explore the power of the likelihood ratio tests (LRT) of neutrality for varying levels of mutation and selection as well as the robustness of the LRT to deviations from the assumption of free recombination among sites. We also discuss the coverage of confidence intervals on the basis of two standard-likelihood methods. We find that the LRT has high power to detect deviations from neutrality and that the maximum-likelihood estimation performs very well when the ancestral states of all mutations in the sample are known. When the ancestral states are not known, the test has high power to detect deviations from neutrality for negative selection but not for positive selection. We also find that the LRT is not robust to deviations from the assumption of independence among sites.

scholarly journals Joint Maximum Likelihood of Phylogeny and Ancestral States Is Not Consistent

2019 ◽  
Vol 36 (10) ◽  
pp. 2352-2357
Author(s):  
David A Shaw ◽  
Vu C Dinh ◽  
Frederick A Matsen
Keyword(s):  
Maximum Likelihood ◽  
Maximum Likelihood Estimation ◽  
Likelihood Estimation ◽  
Branch Length ◽  
Continuous Model ◽  
Model Parameters ◽  
Infinite Length ◽  
Computationally Efficient ◽  
Ancestral States ◽  
Joint Method

Abstract Maximum likelihood estimation in phylogenetics requires a means of handling unknown ancestral states. Classical maximum likelihood averages over these unknown intermediate states, leading to provably consistent estimation of the topology and continuous model parameters. Recently, a computationally efficient approach has been proposed to jointly maximize over these unknown states and phylogenetic parameters. Although this method of joint maximum likelihood estimation can obtain estimates more quickly, its properties as an estimator are not yet clear. In this article, we show that this method of jointly estimating phylogenetic parameters along with ancestral states is not consistent in general. We find a sizeable region of parameter space that generates data on a four-taxon tree for which this joint method estimates the internal branch length to be exactly zero, even in the limit of infinite-length sequences. More generally, we show that this joint method only estimates branch lengths correctly on a set of measure zero. We show empirically that branch length estimates are systematically biased downward, even for short branches.

scholarly journals TreeTime: maximum likelihood phylodynamic analysis

2017 ◽  
Author(s):  
Pavel Sagulenko ◽  
Vadim Puller ◽  
Richard A. Neher
Keyword(s):  
Maximum Likelihood ◽  
Data Sets ◽  
Viral Pathogens ◽  
Data Set ◽  
Set Size ◽  
Likelihood Approach ◽  
Ancestral States ◽  
Analysis Scale ◽  
Phylodynamic Analysis ◽  
Biological Organisms

Mutations that accumulate in the genome of replicating biological organisms can be used to infer their evolutionary history. In the case of measurably evolving organisms genomes often reveal their detailed spatiotemporal spread. Such phylodynamic analyses are particularly useful to understand the epidemiology of rapidly evolving viral pathogens. The number of genome sequences available for different pathogens, however, has increased dramatically over the last couple of years and traditional methods for phylodynamic analysis scale poorly with growing data sets. Here, we present TreeTime, a Python based framework for phylodynamic analysis using an approximate Maximum Likelihood approach. TreeTime can estimate ancestral states, infer evolution models, reroot trees to maximize temporal signals, estimate molecular clock phylogenies and population size histories. The run time of TreeTime scales linearly with data set size.

scholarly journals A comparison of ancestral state reconstruction methods for quantitative characters

2016 ◽  
Author(s):  
Manuela Royer-Carenzi ◽  
Gilles Didier
Keyword(s):  
Maximum Likelihood ◽  
Generalized Least Squares ◽  
Ancestral State Reconstruction ◽  
Likelihood Method ◽  
Reconstruction Method ◽  
Ancestral State ◽  
State Reconstruction ◽  
Evaluation Scheme ◽  
Reconstruction Methods ◽  
Ancestral States

Choosing an ancestral state reconstruction method among the alternatives available for quantita- tive characters may be puzzling. We present here a comparison of five of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares, phylogenetic independent con- trasts and squared parsimony methods. A review of the relations between these methods shows that the first three ones infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) drift. We start by giving the general form of ancestral state distributions conditioned on leaf states under the simulation model. Ancestral distributions are used first, to give a theoretical lower bound of the expected recon- struction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the methods do not perform well as the evolution drift increases; (ii) the maximum likelihood method is generally the most accurate and (iii) not all the distributions of the reconstruction uncertainty provided by the methods are equally relevant.

Maximum Likelihood for Social Science

2018 ◽  
Author(s):  
Michael D. Ward ◽  
John S. Ahlquist
Keyword(s):  
Maximum Likelihood ◽  
Social Science

Das Kommunikationskompetenz-Inventar für Schulleitungen (KKI-SL)

Diagnostica ◽  
2017 ◽  
Vol 63 (3) ◽  
pp. 179-192 ◽  
Author(s):  
Helen Hertzsch
Keyword(s):  
Maximum Likelihood

Zusammenfassung. Gegenstand der vorliegenden Studien ist die Konstruktion und Validierung eines deutschsprachigen Inventars zur Erfassung des Konstrukts Kommunikationskompetenz von Schulleitungen (KKI-SL). Kommunikationskompetenz wird als dreidimensionales Konstrukt (Wissen, Fähigkeiten, Motivation) konzeptualisiert und in ein theoretisches Rahmenmodell eingebettet. Fünf Studien wurden mit deutschen Lehrkräften aller Schularten durchgeführt: Selektion und Kategorisierung der Items via Experten-Rating sowie Exploration der Dimensionalität (N = 169), Kreuzvalidierung der gefundenen Faktorenstruktur (N = 1 354), Test-Retest-Reliabilität (N = 126), konvergente und diskriminante Validität (N = 331) und Kriterienrelevanz (N = 1 023). Itemanalysen und Maximum Likelihood-Faktorenanalysen führten zu einer 3-Faktoren-Lösung (Alterzentrismus, Kommunikationswissen und -bereitschaft, Selbstregulationsfähigkeit) mit guten internen Konsistenzen. Konfirmatorische Faktorenanalysen bestätigten die Struktur mit 14 Items. Die psychometrischen Kennwerte des Inventars waren durchweg gut. Beziehungen zu korrespondierenden Konstrukten belegen die konvergente und divergente Validität des Instruments. Als weiterer Validitätshinweis konnten Zusammenhänge mit relevanten Ergebniskriterien (z. B. Arbeitszufriedenheit) nachgewiesen werden.

Intrafamiliäre Ähnlichkeit von Physischer Anhedonie, Wahrnehmungsabweichungen und Magischem Denken

1999 ◽  
Vol 28 (1) ◽  
pp. 9-17 ◽  
Author(s):  
Thomas D. Meyer ◽  
Martin Hautzinger
Keyword(s):  
Maximum Likelihood ◽  
Sich Eine

Zusammenfassung. Das Ziel der vorliegenden Arbeit besteht darin, durch die Untersuchung des Phänomens der familiären Häufung in Form von intrafamiliären Korrelationen einen Beitrag zur Validität der Schizotypie-Skalen Physische Anhedonie (PA), Wahrnehmungsabweichungen (PAB) und Magisches Denken (MI) zu leisten. 279 Personen und ihren Angehörigen ersten Grades wurden die Schizotypie-Skalen PA, PAB und MI zugeschickt. Die Korrelationen wurden mit Hilfe der Maximum-Likelihood-Methode geschätzt. Für PA und MI fanden sich substantielle Korrelationen zwischen Eltern und ihren Nachkommen, aber keine Ähnlichkeit zwischen den Geschwistern. Bei PAB zeigte sich eine marginale Beziehung zwischen den Werten der Geschwister, aber keine Korrelation zu den Eltern. In allen drei Skalen fanden sich jedoch bedeutsame Korrelationen zwischen den Eltern. Keine Hinweise auf intrafamiliäre Ähnlichkeit bezüglich verschiedener Schizotypie-Indikatoren fanden sich in Form von interindividuellen Kreuzkorrelationen. Die Ergebnisse und ihre theoretische Relevanz werden im Rahmen der bislang existierenden Befundlage zur intrafamiliären Ähnlichkeit bei Schizotypie diskutiert.

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